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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/28713356/a-genotypic-analysis-of-five-p-aeruginosa-strains-after-biofilm-infection-by-phages-targeting-different-cell-surface-receptors
#1
Diana P Pires, Andreas Dötsch, Erin M Anderson, Youai Hao, Cezar M Khursigara, Joseph S Lam, Sanna Sillankorva, Joana Azeredo
Antibiotic resistance constitutes one of the most serious threats to the global public health and urgently requires new and effective solutions. Bacteriophages are bacterial viruses increasingly recognized as being good alternatives to traditional antibiotic therapies. In this study, the efficacy of phages, targeting different cell receptors, against Pseudomonas aeruginosa PAO1 biofilm and planktonic cell cultures was evaluated over the course of 48 h. Although significant reductions in the number of viable cells were achieved for both cases, the high level of adaptability of the bacteria in response to the selective pressure caused by phage treatment resulted in the emergence of phage-resistant variants...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28711508/virulent-and-pathogenic-features-on-the-cronobacter-sakazakii-polymyxin-resistant-pmr-mutant-strain-s-3
#2
Xuerui Bao, Ling Yang, Lequn Chen, Bing Li, Lin Li, Yanyan Li, Zhenbo Xu
Cronobacter sakazakii is a well-known opportunistic pathogen responsible for necrotizing enterocolitis, meningitis and septicaemia in the premature, immunocompromised infants and neonates. This pathogen possesses various virulence factors and regulatory systems, and pmrA/pmrB regulatory system has been identified in a variety of bacterial species. The current study aims to investigate role of pmrA gene in the pathogenicity and virulence characteristics of Cronobacter sakazakii using whole genome sequencing and RNA-seq...
July 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28710619/genome-sequencing-of-steroid-producing-bacteria-with-illumina-technology
#3
Victoria Y Shtratnikova, Mikhail I Schelkunov, Marina V Donova
Illumina technology is widely used for bacterial whole-genome sequencing due to its simplicity, cheapness, reliability, and abundant software for manipulation with raw data. Illumina technology belongs to a second generation of whole genome sequencing that yields great amount of short reads for genome regions. Genomic DNA is fragmented to short pieces. DNA fragments are amplified for signal increasing, and are read using sequencing-by-synthesis. Millions of short reads up to 100-300 bp in length are assembled in continuous sequences...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28706512/comparative-genomics-reveals-high-genomic-diversity-in-the-genus-photobacterium
#4
Henrique Machado, Lone Gram
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28705755/isolation-and-whole-genome-sequence-analysis-of-the-imipenem-heteroresistant-acinetobacter-baumannii-clinical-isolate-hrab-85
#5
Puyuan Li, Yong Huang, Lan Yu, Yannan Liu, Wenkai Niu, Dayang Zou, Huiying Liu, Jing Zheng, Xiuyun Yin, Jing Yuan, Xin Yuan, Changqing Bai
OBJECTIVES: Heteroresistance is a phenomenon in which there are various responses to antibiotics from bacterial cells within the same population. Here, we isolated and characterised an imipenem heteroresistant Acinetobacter baumannii strain (HRAB-85). METHODS: The genome of strain HRAB-85 was completely sequenced and analysed to understand its antibiotic resistance mechanisms. POPULATION: analysis and multilocus sequence typing were performed...
July 10, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28702005/insights-into-a-novel-blakpc-2-encoding-incp-6-plasmid-reveal-carbapenem-resistance-circulation-in-several-enterobacteriaceae-species-from-wastewater-and-a-hospital-source-in-spain
#6
Yancheng Yao, Fernando Lazaro-Perona, Linda Falgenhauer, Aránzazu Valverde, Can Imirzalioglu, Lucas Dominguez, Rafael Cantón, Jesús Mingorance, Trinad Chakraborty
Untreated wastewater, particularly from hospitals and other healthcare facilities, is considered to be a reservoir for multidrug-resistant bacteria. However, its role in the spread of antibiotic resistances in the human population remains poorly investigated. We used whole genome sequencing to analyze 25 KPC-2-producing Enterobacteriaceae isolates from sewage water collected during a 3-year period and three clinical Citrobacter freundii isolates from a tertiary hospital in the same collection area in Spain...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28701744/massively-parallel-whole-genome-amplification-for-single-cell-sequencing-using-droplet-microfluidics
#7
Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama
Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28700648/highly-diverse-and-antimicrobial-susceptible-escherichia-coli-display-a-na%C3%A3-ve-bacterial-population-in-fruit-bats-from-the-republic-of-congo
#8
Kathrin Nowak, Jakob Fahr, Natalie Weber, Antina Lübke-Becker, Torsten Semmler, Sabrina Weiss, Jean-Vivien Mombouli, Lothar H Wieler, Sebastian Guenther, Fabian H Leendertz, Christa Ewers
Bats are suspected to be a reservoir of several bacterial and viral pathogens relevant to animal and human health, but studies on Escherichia coli in these animals are sparse. We investigated the presence of E. coli in tissue samples (liver, lung and intestines) collected from 50 fruit bats of five different species (Eidolon helvum, Epomops franqueti, Hypsignathus monstrosus, Myonycteris torquata, Rousettus aegyptiacus) of two different areas in the Republic of Congo between 2009 and 2010. To assess E. coli pathotypes and phylogenetic relationships, we determined the presence of 59 virulence associated genes and multilocus sequence types (STs)...
2017: PloS One
https://www.readbyqxmd.com/read/28697808/pyrazinamide-resistance-conferring-mutations-in-pnca-and-the-transmission-of-multidrug-resistant-tb-in-georgia
#9
Sarah Sengstake, Indra L Bergval, Anja R Schuitema, Jessica L de Beer, Jody Phelan, Rina de Zwaan, Taane G Clark, Dick van Soolingen, Richard M Anthony
BACKGROUND: The ongoing epidemic of multidrug-resistant tuberculosis (MDR-TB) in Georgia highlights the need for more effective control strategies. A new regimen to treat MDR-TB that includes pyrazinamide (PZA) is currently being evaluated and PZA resistance status will largely influence the success of current and future treatment strategies. PZA susceptibility testing was not routinely performed at the National Reference Laboratory (NRL) in Tbilisi between 2010 and September 2015. We here provide a first insight into the prevalence of PZA resistant TB in this region...
July 12, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28679747/bacterial-physiological-adaptations-to-contrasting-edaphic-conditions-identified-using-landscape-scale-metagenomics
#10
Ashish A Malik, Bruce C Thomson, Andrew S Whiteley, Mark Bailey, Robert I Griffiths
Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where "low-pH" is ~pH 4.3 and "high-pH" is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category)...
July 5, 2017: MBio
https://www.readbyqxmd.com/read/28677247/major-phylum-level-differences-between-porefluid-and-host-rock-bacterial-communities-in-the-terrestrial-deep-subsurface
#11
Lily Momper, Brandi Kiel Reese, Laura Zinke, Greg Wanger, Magdalena R Osburn, Duane Moser, Jan P Amend
Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines, and sampling of deeply-sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply-circulating groundwater and corresponding host rock (at a depth of 1...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28667117/reduced-mutation-rate-and-increased-transformability-of-transposon-free-acinetobacter-baylyi-adp1-isx
#12
Gabriel A Suárez, Brian A Renda, Aurko Dasgupta, Jeffrey E Barrick
The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction...
June 30, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28667105/bacteriocins-of-non-aureus-staphylococci-isolated-from-bovine-milk
#13
Domonique A Carson, Herman W Barkema, Sohail Naushad, Jeroen De Buck
Non-aureus staphylococci (NAS), the bacteria most commonly isolated from the bovine udder, potentially protect the udder against infection by major mastitis pathogens due to bacteriocin production. In this study, we determined the inhibitory capability of 441 bovine NAS isolates (comprising 26 species) against bovine S. aureus Furthermore, inhibiting isolates were tested against a human methicillin-resistant S. aureus (MRSA) isolate using a cross-streaking method. We determined the presence of bacteriocin clusters in NAS whole genomes using genome mining tools, BLAST, and comparison of genomes of closely related inhibiting and non-inhibiting isolates and determined the genetic organization of any identified bacteriocin biosynthetic gene clusters...
June 30, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28666130/tracking-of-listeria-monocytogenes-in-meat-establishment-using-whole-genome-sequencing-as-a-food-safety-management-tool-a-proof-of-concept
#14
Ivan Nastasijevic, Dubravka Milanov, Branko Velebit, Vesna Djordjevic, Craig Swift, Anais Painset, Brankica Lakicevic
Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments...
June 20, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28665263/photobacterium-proteolyticum-sp-nov-a-protease-producing-bacterium-isolated-from-ocean-sediments-of-laizhou-bay
#15
Yan Li, Mingyang Zhou, Fengqing Wang, En Tao Wang, Zongjun Du, Chaoya Wu, Zhenpeng Zhang, Wei Liu, Zhihong Xie
A protease-producing bacterial strain, 13-12T, was isolated from the ocean sediment of Laizhou Bay, PR China and systematically studied. The bacterium was Gram-stain negative, non spore-forming rods, which were motile with two flagella. It was positive for oxidase, the hydrolysis of starch, agar and gelatin, and for nitrate reduction. It was negative for catalase, esterase and the degradation of CM-cellulose. Optimum growth was observed at 28 °C, pH 6.5-7.0 and in the presence of 2-3 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene, and whole genome data, affiliated it to the genus Photobacterium...
June 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28663304/determinants-of-post-prandial-plasma-bile-acid-kinetics-in-human-volunteers
#16
Jarlei Fiamoncini, Andrianos M Yiorkas, Kurt Gedrich, Milena Rundle, Sanne I Alsters, Guus Roeselers, Tim J van den Broek, Thomas Clavel, Ilias Lagkouvardos, Suzan Wopereis, Gary S Frost, Ben van Ommen, Alexandra I F Blakemore, Hannelore Daniel
Bile acids (BA) are signaling molecules with a wide range of biological effects, also identified amongst the most responsive plasma metabolites in the post-prandial state. We here describe this response to different dietary challenges and report on key determinants linked to its inter-individual variability. Healthy men and women (N=72, 62 ± 8 years) were enrolled into a 12-week weight loss intervention. All subjects underwent an oral glucose tolerance test (OGTT) and a mixed meal tolerance test (MMTT) before and after the intervention...
June 29, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28662764/pulsenet-international-vision-for-the-implementation-of-whole-genome-sequencing-wgs-for-global-food-borne-disease-surveillance
#17
Celine Nadon, Ivo Van Walle, Peter Gerner-Smidt, Josefina Campos, Isabel Chinen, Jeniffer Concepcion-Acevedo, Brent Gilpin, Anthony M Smith, Kai Man Kam, Enrique Perez, Eija Trees, Kristy Kubota, Johanna Takkinen, Eva Møller Nielsen, Heather Carleton
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives...
June 8, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28657170/the-past-decade-in-bench-research-into-pulmonary-infectious-diseases-what-do-clinicians-need-to-know
#18
REVIEW
Simon Finch, Holly R Keir, Alison J Dicker, James D Chalmers
Respiratory infections are primarily treated with antibiotics, drugs that are mostly inexpensive and have been widely available since the 1940s and 1950s. Nevertheless, despite antibiotics, the burden of disease in pneumonia, bronchiectasis, cystic fibrosis, COPD and rare respiratory infections remains exceptionally high. There is an urgent need for translational studies to develop new treatments or new biomarkers to improve outcomes in these conditions. The 'translational gaps' between bench science and clinical practice are particularly challenging in respiratory infections...
June 28, 2017: Respirology: Official Journal of the Asian Pacific Society of Respirology
https://www.readbyqxmd.com/read/28639162/bacterial-genome-sequencing-in-clinical-microbiology-a-pathogen-oriented-review
#19
REVIEW
F Tagini, G Greub
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing...
June 21, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28630127/deciphering-function-of-new-gonococcal-vaccine-antigens-using-phenotypic-microarrays
#20
Benjamin I Baarda, Sarah Emerson, Philip J Proteau, Aleksandra E Sikora
The function and extracellular location of cell envelope proteins make them attractive candidates for developing vaccines against bacterial diseases, including challenging, drug-resistant pathogens such as Neisseria gonorrhoeae Proteomics-driven reverse vaccinology delivered multiple gonorrhea vaccine candidates; however, the biological functions of many of them remain to be elucidated. Herein, the functions of six gonorrhea vaccine candidates - NGO2121, NGO1985, NGO2054, NGO2111, NGO1205, and NGO1344 - in cell envelope homeostasis were probed using phenotype microarrays with 1,056 conditions and a ΔbamE mutant (Δngo1780) as a reference of perturbed outer membrane integrity...
June 19, 2017: Journal of Bacteriology
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